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GeneBe

10-16695157-TG-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The NM_012425.4(RSU1):c.599-3del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., cov: 17)

Consequence

RSU1
NM_012425.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 2.33

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BP6
?
Variant 10-16695157-TG-T is Benign according to our data. Variant chr10-16695157-TG-T is described in ClinVar as [Likely_benign]. Clinvar id is 1328202.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RSU1NM_012425.4 linkuse as main transcriptc.599-3del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000345264.10
RSU1NM_152724.3 linkuse as main transcriptc.440-3del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
RSU1XM_047425617.1 linkuse as main transcriptc.598+57381del intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSU1ENST00000345264.10 linkuse as main transcriptc.599-3del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_012425.4 P1Q15404-1

Frequencies

GnomAD3 genomes
AF:
0.000195
AC:
25
AN:
128178
Hom.:
0
Cov.:
17
show subpopulations
Gnomad AFR
AF:
0.000232
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000154
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000281
Gnomad FIN
AF:
0.000293
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000183
Gnomad OTH
AF:
0.000578
GnomAD4 exome
AF:
0.00964
AC:
10055
AN:
1043536
Hom.:
4
AF XY:
0.00977
AC XY:
5064
AN XY:
518274
show subpopulations
Gnomad4 AFR exome
AF:
0.00281
Gnomad4 AMR exome
AF:
0.0148
Gnomad4 ASJ exome
AF:
0.0118
Gnomad4 EAS exome
AF:
0.00519
Gnomad4 SAS exome
AF:
0.00902
Gnomad4 FIN exome
AF:
0.0137
Gnomad4 NFE exome
AF:
0.00958
Gnomad4 OTH exome
AF:
0.0109

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Likely benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs56715139; hg19: chr10-16737156; API